java.lang.Exception: ERROR ERROR ERROR: Reached end of bam file, there are 22763461 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file. (Example Orphaned Read Name: D00118:263:C89KTANXX:4:1209:7544:95127)

There are no available Samebug tips for this exception. Do you have an idea how to solve this issue? A short tip would help users who saw this issue last week.

  • GitHub comment 22#247979622
    via GitHub by hartleys
    ,
  • Issue with spike-ins
    via GitHub by royfrancis
    ,
    • java.lang.Exception: ERROR ERROR ERROR: Reached end of bam file, there are 22763461 orphaned reads, which are marked as having a mapped pair, but no corresponding pair is found in the bam file. (Example Orphaned Read Name: D00118:263:C89KTANXX:4:1209:7544:95127) at internalUtils.Reporter$.error(Reporter.scala:269) at internalUtils.commonSeqUtils$$anon$2.next(commonSeqUtils.scala:728) at internalUtils.commonSeqUtils$$anon$2.next(commonSeqUtils.scala:699) at internalUtils.stdUtils$IteratorProgressReporter$$anon$4.next(stdUtils.scala:302) at scala.collection.Iterator$class.foreach(Iterator.scala:743) at internalUtils.stdUtils$IteratorProgressReporter$$anon$4.foreach(stdUtils.scala:296) at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1055) at qcUtils.runAllQC$.run(runAllQC.scala:774) at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:502) at runner.runner$.main(runner.scala:92) at runner.runner.main(runner.scala)
    No Bugmate found.